The bugs identified by Euphoniac were taken care of (thanks again for the thorough look).
Also - I removed level-scaling from common enemies (Boss level were always hard-coded). There is still a level range for each area, but you will cap out much quicker than before. It will make gaining levels much more rewarding for you!
I know that sometimes updates mess with your save files. I'll try to keep the updates meaningful and at a non-invasive rate as to reduce this undesired effect.
Thanks!